Integration of end-of-life options as a design criterion in methods and tools for ecodesign

Ecodesigning a product consists (amongst other things) in assessing what its environmental impacts will be throughout its life (that is to say from its design phase to its end of life), in order to limit them. Some tools and methods exist to (eco)design a product, just like methods that assess its environmental impacts (more often, a posteriori). But it is now well accepted that these are the early design decisions that will initiate the greatest consequences on the product’s end-of-life options and their impacts. Thus, the present work aims at analysing traditional design tools, so as to integrate end-of-life possibilities in the form of recommendations for the design step. This proposal will be illustrated by means of a wind turbine design.EcoSD networ

Structure determination of Split-soret Cytochrome from a Desulfovibrio species isolated from a human abdominal abcess

The determined structure of the split-soret cytochrome (SSC) isolated from Desulfovibrio desulfuricans ATCC 27774 (D.d.) revealed a new Heme arrangement, which suggests that this protein constitutes a new cytochrome class.. SSC is a 52.6kDa homodimer containing four hemes at one end of the molecule. In each monomer the two hemes have their edges overlapped within van der Waals contacts. The polypeptide chain of each monomer supplies the sixth ligand to the heme-iron of the other monomer. A similar protein was recently purified from a homologous Desulfovibrio clinical strain isolated from an abdominal wall abscess in human patient2. Crystals of this SSC were grown using vapour diffusion method in the presence of agarose gel. Diffraction data were collected using X-ray synchrotron radiation at the ESRF, beamline, ID 14-1. The structure will be solved by molecular replacement using the structure of the D.d. as a starting model

A Genetic Linkage Map Using an F1 Population in Rubber Tree (Hevea brasiliensis) based on microsatellite markers. P0527

The construction of molecular gene linkage map in Hevea requires specific methodology because of high heterozygosity. Unlike annual crops, a cross between two heterozygous parents in Hevea can yield information up to four alleles, which are segregated further. The mapping population was a full-sib progeny (F1 progeny) derived from a cross between the cultivars PB217 and PR255. A set of 603 microsatellite primer pairs was tested for polymorphism the two parents and six F1 progenies genotypes. Linkage map was obtained using OneMap (Margarido et al., 2007). LOD Score 4.5 and recombination fraction of 0.40 was considered to determine linkage between markers. In total, 288 marks were genotyped (230 SSR genomic loci and 58 EST-SSR). The map consists of 288 markers, distributed in 23 linkage groups (LG) and 2833.8 cM in length with an average genetic distance of 9.8 cM between adjacent markers. The largest group has 228.7 cM (29 markers) and the smallest has 10.3 cM (4 markers). SSRs provide powerful tool for genetic linkage map construction that can be applied for identification of QTL. Importantly, the marker linked to the QTL can be further applied to MAS in rubber tree breeding program for selecting plant that contains desirable phenotype. The map is not saturated enough and some chromosome regions could not be linked. The chromosome number accepted today, for most Hevea species, is 18 (2n=36). The present map will be used for yield rubber QTL mapping and other important economical characteristics. (Texte integral

Genomic selection in rubber tree breeding: A comparison of models and methods for managing G×E interactions

Several genomic prediction models combining genotype × environment (G×E) interactions have recently been developed and used for genomic selection (GS) in plant breeding programs. G×E interactions reduce selection accuracy and limit genetic gains in plant breeding. Two data sets were used to compare the prediction abilities of multienvironment G×E genomic models and two kernel methods. Specifically, a linear kernel, or GB (genomic best linear unbiased predictor [GBLUP]), and a nonlinear kernel, or Gaussian kernel (GK), were used to compare the prediction accuracies (PAs) of four genomic prediction models: 1) a single-environment, main genotypic effect model (SM); 2) a multienvironment, main genotypic effect model (MM); 3) a multienvironment, single-variance G×E deviation model (MDs); and 4) a multienvironment, environment-specific variance G×E deviation model (MDe). We evaluated the utility of genomic selection (GS) for 435 individual rubber trees at two sites and genotyped the individuals via genotyping-by-sequencing (GBS) of single-nucleotide polymorphisms (SNPs). Prediction models were used to estimate stem circumference (SC) during the first 4 years of tree development in conjunction with a broad-sense heritability (H2) of 0.60. Applying the model (SM, MM, MDs, and MDe) and kernel method (GB and GK) combinations to the rubber tree data revealed that the multienvironment models were superior to the single-environment genomic models, regardless of the kernel (GB or GK) used, suggesting that introducing interactions between markers and environmental conditions increases the proportion of variance explained by the model and, more importantly, the PA. Compared with the classic breeding method (CBM), methods in which GS is incorporated resulted in a 5-fold increase in response to selection for SC with multienvironment GS (MM, MDe, or MDs). Furthermore, GS resulted in a more balanced selection response for SC and contributed to a reduction in selection time when used in conjunction with traditional genetic breeding programs. Given the rapid advances in genotyping methods and their declining costs and given the overall costs of large-scale progeny testing and shortened breeding cycles, we expect GS to be implemented in rubber tree breeding programs

L'entretien de recherche avec des journalistes Editorial

International audienceThis is true of our first issue on interviews, a methodology which cuts across the fields of human and social sciences. We invite you to read it and consider what this particular research approach yields from real people in different disciplinary—and cultural—contexts

Genome sequencing of a Hevea brasiliensis for single nucleotide polymorphism discovery

The rubber tree (Hevea spp.), is the primary plant used in natural rubber production. Historically, the breeding of rubber trees has been based on techniques involving statistics and quantitative genetic approaches to determine the best genotypes to be used as new cultivars. The discovery of molecular genetic markers has provided new possibilities for characterizing genotypes for the purpose of identifying cultivars, analyzing genetic diversity, establishing relationships between agricultural traits and genetic factors (QTLs), and identifying genes of interest. The application of next generation sequencing technology has brought a new opportunity for high throughput single nucleotide polymorphism (SNP) discovery. Knowledge about SNPs markers is extremely important in the development of genotyping assays, allowing improvements in plant breeding through marker-assisted selection. In this project, we carried out genomic sequencing of two rubber tree cultivars. The DNA libraries were constructed for two cultivars of rubber tree (two from GT1 and two from RRIM701) and sequenced in Illumina plataform. The resulting short reads (72 bp) were submitted to quality filtering and then were de novo assembled using the CLC software. Next, Burrows-Wheeler Aligner (BWA) aligned short reads back to assembled contigs, and Freebayes was used to perform variant calling and snp detection. Genotype likelihoods were computed and variable positions in the aligned reads were compared to the reference contigs. Using the varFilter command of VCFutils script, SNPs were filtered only for positions with a minimal mapping quality (-Q) and coverage (-d) of 30 and 10 respectively. Unique and shared SNPs among the two cultivars were extracted with the VCFtools software. SNPs located in contigs containing open reading frames (ORFs) ?200 bp were also extracted using transdecoder script. A total of 10,993,648 reads were obtained. Only 10,071 contigs were retained after assembly and removal of singletons and repetitive regions. The contig length median was 3078 bp (N50), and GC content was 35.4%. After the step of clustering and homology search against H. brasiliensis draft genome via blastx, the remaining 6,995 contigs were used as reference for mapping and SNP calling. In total, Freebayes detected a total of 59,116 (39,455 transitions and 19,812 transversions, Ts/Tv=1,99) different heterozygous SNP position in sequences using the stringent parameters. Of these SNPs, 41,621 (70.4%) were found in contigs containing predicted open reading frames (ORFs). Regarding different genotypes, 19,118 putative SNPs were found in GT1 and 25,360 in RRIM701. These cultivars shared 14,568 SNPs positions. The results show that it is possible to combine next generation sequencing data combined with high-density SNP detection methods to discover large numbers of putative SNPs in Hevea brasiliensis, providing a framework for further population genomic studies to identify the molecular basis underlying phenotypic variation of relevant traits in a non-model species. Financial Support: FAPESP. (Résumé d'auteur

L'entretien de recherche avec des journalistes Propos introductifs

International audienceL a mobilisation des entretiens dans les recherches sur le journalisme est une pratique courante, rapidement évoquée dans les écrits des chercheurs, comme si l'entre-tien était un outil transparent, sur lequel il ne semble pas, ou plus, nécessaire de s'arrêter. L'essentiel semble de produire puis de restituer un matériau, des données qui doivent faire levier dans des processus de dé-monstration et de dévoilement de réels médiatiques contrastés. L'analyse des spécificités des entretiens avec des professionnels des médias nous a semblé manquer aux recherches menées dans différentes disciplines ayant pour objet commun le journalisme. C'est ce manque et ce « creux épistémologique et méthodologique » que nous avons voulu interroger et chercher à combler. Le dossier est né d'une journée d'étude sur la méthodologie de recherche en journalisme, tenue à l'Université de Brasilia le 28 avril 2011. Intitulée L'entretien de recherche avec des journalistes : miroir, fiction et transferts ? cette rencontre clôturait un colloque international portant sur les mutations structurelles du journalisme (Actes du colloque, 2011). Elle entendait confronter des chercheurs de plusieurs disciplines issus de trois territoires (France, Canada, Brésil), spécialistes de la méthodologie de l'entretien, aux publics du colloque, experts pour leur part des études sur le journalisme. Ces travaux ont ensuite été complétés par un appel à proposition auprès de chercheurs de diverses disciplines

Adaptation of Agro-IBIS model for Eucalyptus carbon budget estimation at regional level- a case study in Sao Paulo State, Brazil

Highly productive fast-growing Eucalyptus plantations cover more than 5 million hectares in Brazil and exhibit very dynamic carbon fluxes throughout their 6-7 year rotations. These plantations quickly shift from C sources at the beginning of the rotation to large C sinks until harvest. In order to get a model simulating carbon pool and fluxes for both Eucalyptus plantations and other crops, we integrated several sub-models of the Eucalyptus-dedicated Generic Decomposition And Yield Model (G'DAY) into the large scale and multi-cover model Agro-IBIS (Integrated Biosphere Simulator). The G'DAY model was previously parametrized and validated using large experimental datasets obtained in commercial eucalypt plantations in the state of Sao Paulo. Implementing an Eucalyptus plantation cover type within AgroIBIS. which had no Plant Functional Type dedicated to fast-growing forest plantations, required important changes in the carbon allocation turnover sub-models. This study included three phases: (1) the computational modification of AgrolBIS; (2) the model parametrization, calibration and validation using data from intensively monitored sites or inventories datasets; and (3) model application at regional scale using sets of parameters which were considered to be constant in space and/or time based on data from the local experiments, and other sets of parameters which could vary spatially. Carbon fluxes of Eucalyptus plantations were simulated at the regional scale, and their inter-annual and spatial variabilities were analysed. Such spatial and multiannual quantification of carbon fluxes at large scales brings a better understanding of these forest ecosystems on global carbon cycling, which is a prerequisite to support policy decisions

Population genetic structure based on microsatellite markers in rubber tree (Hevea brasiliensis) germplasm collection : [P483]

Hevea brasiliensis is native to the Amazonian rain forest and an important source of natural rubber. All high-yielding cultivars of rubber tree in the world originated from breeding programs initially developed in Southeast Asia with a very narrow genetic basis. Germplasm diversity is the mainstay for crop improvement and genetic dissection of complex traits. Understanding genetic diversity, population structure, and the level and distribution of linkage disequilibrium (LD) in target populations is of great importance and a prerequisite for association mapping. A part of germplasm collection is used here and 192 accessions from Agronomic Institute of Campinas (IAC) and Eduard Michelin Plantation were screened with 15 microsatellite markers (SSR). Genomic DNA was extracted from young leaf tissues and was amplified by PCR. The Mean number of alleles per locus, mean expected heterozygosity and polymorphic information content across all accessions were 16.58, 0.90, and 0.89, respectively. The STRUCTURE analyses identified three subgroups among this population panel. The consensus neighbor-joining tree resulted in three clusters that generally agreed with three subgroups from the structure analyses. Overall, the results suggest that these populations can be exploited for assess the extent and genome-wide distribution of linkage disequilibrium (LD). Additional molecular markers, including more SSRs and single nucleotide polymorphisms (SNPs), should be used to provide better coverage of the genome and more genotyping should be initiated with the germplasm collection. In addition, the germplasm collection can also be used in the selection of parents for future crosses, based on genetic distance of the accessions. (Résumé d'auteur